Monday, August 28, 2006

Snakes on my blog

After going to watch "Snakes on a Plane" at my local multiplex, I was inspired to do some fact-checking on the screenplay by running a quick search of the literature.
(Here come the comments about selling out on blog topics too early in my fledgling career.)
My search engine of choice was PubMed, a government service with millions of journal article abstracts searchable by topic, author, etc.
To read about the premise of this cult thriller, click here. In short, the snakes on the plane became extremely aggressive and started attacking people because of a concentrated pheromone that was sprayed onto the passengers' leis. (The plane was en route to LA from Hawaii).
Here are some of the more interesting tidbits I dug up:
the ref: Science 1989, 245, 290-3.
The female pheromone of the Canadian red-sided garter snake is an intricate concoction of nonvolatile saturated and monounsaturated long-chain methyl ketones, and the corresponding male pheromone contains squalene (see figure), a compound I first learned about in my chemistry classes because of its role as a key intermediate in cholesterol biosynthesis.

So, did the mafia goons just spray one chemical onto those leis, or was it an "all purpose pheromone" that would "do it" for all of about twenty or thirty different species of snakes that were wreaking havoc on the plane? The snakes were from all over the world, as the actor playing the snake expert told us numerous times. I'd guess their pheromones were slightly different, but maybe not enough for it to matter?

Another thing: It's counterintuitive to me that pheromones from the opposite sex would trigger aggression. (I know, different strokes for different folks, but still...) It would make more sense that a pheromone from a member of the same sex would get the competitive juices flowing.
A 2002 paper suggests that a certain lizard species relies mainly on scent to determine the gender of an intruder. The authors experimentally manipulated the body markings and odor of the lizards in order to learn more about the interplay between sight and smell. Among other things, they observed that male snakes responded aggressively to a snake that smelled male, even if it was painted to look like a girl.
that ref was: Aggressive Behavior 2002, 28, 154-163.

Does that mean that to minimize confusion, all the snakes on that plane had to be the same sex? Or at the very least, there couldn't be any Black Adders.

I'll stop now, because this may just be the most thought anyone's ever given to the movie after having seen it, and that'll spoil the mood.


Friday, August 25, 2006

Quark Park: All of the Charm, a little of the Strange

If you're in the Princeton area this fall, be sure to take some time for reflection at Quark Park, an innovative new sculpture garden opening September 8th. I read about the park here, here, and here, and there are plenty of links to other stories at the official Quark Park site.
A quark is one of the most fundamental units that make up matter (all the "stuff" in the universe around us). They're part of what atoms are composed of. (Yes, that's TINY! Quarks can't be seen.) The system that particle physicists came up with for naming quarks is one of the most interesting I've come across. I'm drastically oversimplifying the system (see here for more detail) but quarks can have any one of six "flavors":
The exhibits interweave the visions of local artists and scientists, and are meant to educate as well as inspire. For example, Princeton President Shirley Tilghman teamed up with a sculptor and an engineer to bring to life the complex networks through which we process smells. U.S. Congressman (and card carrying physicist) Rush Holt joined forces with emeritus physics professor Freeman Dyson and an architect to create a display about alternative forms of energy. The nonprofit group behind the park, Princeton Occasions, is still seeking funding to erect a stage in the park, which will be used for science demos, lectures, and performances. I work with the Chemistry department's outreach program and I think it would be lots of fun to electrocute pickles and make liquid nitrogen ice cream in a garden setting.
Unfortunately, the vacant lot where Quark Park stands is slated for condos in early 2007, so the park is only temporary (until late October or November, say the articles). Visit it while you can!


Monday, August 21, 2006

Platensimycin Redux

Last Saturday, the Journal of the American Chemical Society published the isolation and structure determination of the natural product antibiotic platensimycin.
The paper can be found here.
I posted about this compound at this link. The new paper demonstrates that the potentially reactive alpha, beta-unsaturated ketone (enone, highlighted in red in figure) does not appear to contribute to platensimycin's chemical mechanism of action, but the conformation of the ring containing the enone does seem to play a role.
Platensimycin adsorbs well to the drying agent magnesium sulfate, perhaps a little too well, because it was impossible to recover product from it. The ortho-hydroxybenzoic acid chelates the magnesium. No problem with sodium sulfate, though. You called it, Jack.


Sunday, August 20, 2006

Momma said knock you out

I didn't want to miss the chance to blog about an anesthesia paper I saw in ACS Chemical Biology. :)
The ref:
ACS Chem. Biol. 2006, 1, 377-384.

A synthetic organic chemist may scoff at the structural simplicity of anesthetics like halothane and isoflurane (see figure), but there's no doubt that the effects they have on our physiology are very complex. These compounds bring on amnesia (unconsciousness/ unawareness), analgesia (pain relief), and paralysis, and all of these effects are completely reversible. When a new anesthetic emerges, it's important to figure out the molecular mechanisms behind its activity, but researchers are still very much in the dark in this area.

It doesn't help matters that these molecules are challenging to work with in the lab. They're volatile (evaporate easily), and they don't have a very strong binding affinity for their target(s). The latter is a good thing since you want your anesthetic to wear off!

There is some data available about binding sites and targets for older anesthetics called haloalkanes (halothane is in this category), but those molecules really aren't used in human patients anymore because of their toxicity profiles. The goal of this paper is to develop a tool to get the same kind of data on the stuff we're actually using, the haloethers (like isoflurane).

To solve the low binding affinity problem, Xi and colleagues designed an isoflurane mimic (see figure) that's photoactivatable. The molecule resembles isoflurane, but it contains some chemical bonds that will break down when you shine light of a certain energy on them. Once that happens, what's left is a reactive species that they anticipated would latch onto a target, allowing them to better examine the interaction.

The conclusion of the paper was that the photoactivatable isoflurane mimic is a valid tool for research in this area. It behaves similarly to isoflurane in the petri dish and in animal tests, and binds to a known isoflurane target in a very similar place.

I did notice a couple of minor nomenclature errors in the paper: Isoflurane is 1-chloro-2,2,2-trifluoroethyl difluoroMETHYL ether, and the analogous correction also goes for desflurane.

The reactive group that the researchers engineered is called a carbene. An explanation of what that is is beyond the scope of this blog, but not of this website. Maybe someone who remembers carbene reactivity better than I do can answer the question they pose in the text: Is there an amino acid residue with which the UV-generated carbene won't react? They propose mutagenesis experiments, and I'm sure you can just buy a kit somewhere that'll take care of that, but there must be some references are already out there on this. The whole train of thought began when they didn't see the expected reactivity with tyrosine. It seems like they're trying to determine whether it's a question of intrinsic reactivity or just the molecule's "fit" in the cavity.

To do: the authors mentioned that the more old-school haloalkane anesthetics like halothane were used to fish out potential targets for interaction through photolabeling in complex mixtures. I'd like to see that experiment done with this analog. This kind of experiment has already been done in many other systems (for example, see here). I guess it just depends on how easily they can incorporate a visualization element.


Thursday, August 10, 2006

I work for peanuts

I visited NYC after work last Saturday and supped at Spice, a Thai restaurant chainlet with a couple of locations in the city (I was on the Upper East Side). The decor was mod and minimalist and the food was great, but we limited our selection because one of my friends is highly allergic to peanuts.
Nature News ran an article a few weeks back that sheds a little more light on the mechanism behind anaphylactic shock. This is the most severe form of allergy, leading to a drop in blood pressure that is fatal if left untreated. We can treat someone who is in shock with a shot of epinephrine ("epi"), but this is more of a patchup; it doesn't get at the root of the problem and it can't prevent shock.
Here's the paper:
J. Clin. Invest. 2006, 116, 2244-2251.
In a nutshell (ha ha), the researchers confirmed previous reports that nitric oxide pathways are responsible, but the source of the nitric oxide wasn't the one they were expecting. They also pinpoint an often-studied signaling pathway (the PI 3-kinase pathway) as one of the orchestrators behind the whole nitric oxide-mediated shock response.
The PI 3-kinase pathway is involved in a large number of fundamental processes in our cells. A kinase is an enzyme that puts a tag (a phosphate group) on some other protein. The body uses phosphate groups as switches, adapters or handles for a ridiculous number of things. It's one of the ways the body physically transfers and amplifies a message. The authors conclude that it might be useful to look at the PI 3-kinase pathway as a way to intercept the shock response.
To demonstrate the involvement of PI 3-kinase, the researchers used wortmannin, my personal favorite inhibitor of PI 3-kinase. Wortmannin is a natural product made by fungi and it reacts with the business end of PI 3-kinase. For the mechanistically minded, I've included a figure.

The PI 3-kinase enzyme has a critical lysine involved in the phosphate transfer reaction, and wortmannin knocks that bad boy out of commission.


Wednesday, August 09, 2006

Promiscuous G, you're teasing me.

I read this paper for a literature meeting nearly a month ago and I had meant to blog about it at the time. Here's the reference:
"Obestatin, a Peptide Encoded by the Ghrelin Gene, Opposes Ghrelin's Effects on Food Intake"
Science 2005, 310, 996-999.
Obestatin is a hormone that suppresses food intake and weight gain in mice (thanks to Harriet for the picture of the cute little mousie), so you can imagine that a lot of news outlets picked up the story when the paper came out last year. The message there was that finding obestatin provides a new drug target that could allow researchers and physicians to rein in that 10 AM candy bar craving in the not-too-distant future.

The work was fascinating to many researchers, not as the next big obesity cure, but because ghrelin and obestation come from the same gene and appear to have opposite effects! (Ghrelin increases body weight in mice.) The paper's authors first had a hunch that obestatin would exist because they performed a computer search of extensive genome sequence data for genes that look like they code for hormones. This touches off a debate on how much of an effect genomics has really had on the way we conduct research. See this post at In the Pipeline for commentary.

When I read this paper, I was drawn to the discovery that obestatin activates something called an "orphan G-protein-coupled receptor". Receptors are proteins that relay signals in the body in order to achieve some downstream effect, like muscle contraction. The human genome sequence has turned up a couple hundred genes that encode "G-protein-coupled receptors", a specific family of receptors with a track record of being valuable drug targets. Researchers don't yet know what interacts with "orphan receptors", but they'd eventually like to correlate them to a particular pathway or disease, so that they can eventually develop new and better drugs. That's why obestatin was such a big deal in the health field.

I guess this paper got me to thinking, "Isn't there a more proactive way to find the ligands (partners) for these orphan receptors instead of just waiting around for someone to publish papers like this one a couple of times a year?"

There are several ways that researchers go about this systematically. Scientists can take a little of the guesswork out of what the ligand is based on how similar the orphan receptor is to the ones we already know. Screening lots of potential partners at once is possible by coupling the receptor-ligand interaction to some kind of readout. The "adapter" they use is a G protein. Yes, these receptors are coupled to a G protein that sends out a message on its behalf. That's where the name "G-protein-coupled receptor" comes from.

So, why a promiscuous G protein? Promiscuous G's can speak for a wide range of receptors. It's much easier to set up the experiment if you don't have to change multiple components. Just get the new receptor that you want to test and all the other pieces are ready to go.

Unfortunately, there's no "universal adapter" quite yet. These screens are used often in drug discovery, but for now, scientists are getting by with an assortment of naturally occurring promiscuous G proteins and a few that they've engineered in the lab, and having to pick the one that works best for their system.

See these refs:
TRENDS Pharmacol. Sci. 2005, 26, 595-602.
Annu. Rev. Pharmacol. Toxicol. 2004, 44, 43-66.
Receptors and Channels 2002, 8, 297-308.
TRENDS Pharmacol. Sci. 2001, 22, 560-564.


Friday, August 04, 2006

Cramming for the test

Steroids are in the spotlight this weekend, as we prepare for the results from the test of Floyd Landis's "B" sample. The issue at hand: Landis, the American winner of this year's Tour de France, tested positive for testosterone use after stage 17 of the Tour, which is where he mounted a dramatic comeback to retake the lead.

aside: Stephen Colbert's response a few days back, "Of course he tested high for testosterone! He's a red-blooded American!"

Cycling authorities state that Landis had provided a backup urine sample from that stage that is being tested as we speak to confirm the results and rule out contamination, etc. All this drama in a Tour de France already tainted by a doping scandal.

Testing for anabolic steroid abuse is a complicated process. Anabolic, by the way, loosely translates to constructive metabolism, "building up" or "reconstructing". Testosterone occurs naturally in the human body, but the levels vary enough from person to person that it's difficult to gauge what is normal. Instead, authorities test the ratio of testosterone to epitestosterone, nicknamed the T/E ratio. The chemical structures of the two are actually very similar, but right now, it's not clear what function epitestosterone might have. We know a lot about what testosterone does. Amazing what one little -OH group is worth.

There is a much better post here about the intricacies of conditions leading to low epitestosterone, anti-doping legislation and the testing involved.

An alternate test exists which uses mass spectrometry to distinguish synthetic testosterone from natural testosterone. A coworker of mine said that this had been mentioned in a news broadcast (can't remember where) and like good scientists, we were skeptical. Huh? How could that work? The masses should be the same! Turns out, it was just a case of oversimplification. Most people probably couldn't care less about the details, but I hold you to a higher standard, gentle reader.

The mass spectrometer can detect differences in the ratio of the two stable carbon isotopes, 13C and 12C. Isotopes of the same element have slightly different masses. Synthetic testosterone contains less 13C than the naturally occurring kind. Fox News says that most synthetic testosterone comes from soy. This post doesn't mention soybeans specifically, but goes into the details of how different plants end up with different 13C content based on how exactly they take in nutrients from photosynthesis.

The problem I see with measuring a ratio is that Landis's high reading could be due to high testosterone levels or a low excretion of epitestosterone. Also, I would think that if this were a case of doping, why couldn't he just administer epitestosterone, too? Anybody know the pharmacokinetic data for these? Maybe one's excreted much faster?

This paper describes how to use mass spectrometry to detect artificial epitestosterone.
Clinical Chemistry 2002, 48, 629-636.

It takes a little creativity to think of new tests, as there will always be new ways to mask cheating. Slightly off-topic: A college friend wrote her undergrad thesis in collaboration with the NJ State Police; she was trying to find a better way to test for gamma-hydroxybutyrate, a date rape drug.

Another test I thought was cool: Physicians can measure the levels of insulin C-peptide in patients with type 1 diabetes to see whether the pancreas is making any insulin on its own. The insulin that diabetics inject into their bodies is made without C-peptide, because it's not necessary for the insulin to work.

From MedLine Plus:
When insulin is synthesized by the beta cells of the pancreas, it is produced as a large molecule (a propeptide). This molecule is then split into two pieces: insulin and C-peptide. The function of C-peptide is not known.
Normal values in a patient requiring insulin injections indicate that the person's body is still producing some insulin. Normal values in a patient who has low blood sugar indicate that the patient is making too much insulin.
Low values (or no Insulin C-peptide) indicate that the person's pancreas is producing little or no insulin.
Update 8/9/06
I hadn't noticed that In the Pipeline blogged this a few days before. Read the post for some insight as to why the soy plant has a lower 13C content.